Free mode : if you press this the "figure" objects will be manually positioned by the user. The layout of the "figure" content is handled by EZFig. If you do not activate this mode all the layout is handled by EZFig.

Nb : please note that the content of the "available actions" panel depends on current selection type (see the "Dynamic menus" section).

3.3) Importing files from ImageJ/FIJI

Select "import single image from ImageJ" if you want to import the currently displayed image. Alternatively select "import stack from ImageJ", if you want to be able to activate/deactivate channels, change channel color, or browse slices or frames of the image.

4) Load/Save EZFig files

EZFig has its own native format (.ezf). It is very important to always save the figure in “ezf” format as it is the only format that can be re-edited by EZFig, all other export formats cannot be dynamically modified. EZFig is backward compatible width ScientiFig, i.e. it can read ScientiFig files (.yf5m). The opposite is not true, ScientiFig cannot read .ezf files.

4.1) Load .ezf Files

The simplest way to load an ezf or a yf5m file is to drag and drop it onto EZFig.

4.2) Save .ezf files

Press “File > Save as...” to save an “ezf” file. Note that if the figure contains stacks, they will be saved in a folder with the same name as the “ezf” file with an extra .files. Please always store the .ezf and the .ezf.files folder together, otherwise stack data will be lost. Nb: You can use the Ctrl/Cmd + S shortcut to save.

5) Exports

5.1) Direct exports

To export a Figure, press "File>Export as..." and select one of the export formats available. Please note that exported files cannot be further edited by EZFig, so it is particularly important to also "save" your figures (see Section “Save .ezf files”).

6.1) The basics of object selection in EZFig

Clicking the upper right image selects the whole “Figure”, the highest level container in EZFig (note the yellow color of the selection and the "Figure" keyword drawn in the center of the figure object)

Clicking the upper right image again selects a "Panel/Montage", yet another lower level container. (Note the magenta color of the selection and the "Panel" keyword drawn in the center of the Panel object).

Clicking the upper right image again finally selects the image, the lowest level object in the figure hierachy. (Note the red color of the selection and the "Img" keyword drawn in the center of the “image” object).

Note that the options in the panel located at the right of the software change with selection type. Options will also change depending on whether it is a single selection or multiple selection. Multiple selection is obtained by maintaining the Ctrl/Cmd key while clicking.

Summary of the hierarchy of objects in EZFig and their associated colour selection scheme :

7) Menus

7.1) File

Open : prompts a dialog to load .ezf (EZFig) and .yf5m (ScientiFig) files. You can also simply use drag and drop (DND).

Import images : prompts a dialog to import raster/bitmap or vector images to EZFig. You can also use DND (please also see the "Imports" section).

Import single image from ImageJ : First open an image in ImageJ, select the channels you want to display, the contrast settings, the slice and or frame you want to insert in a figure. Then press this button to import the current display to EZFig. (Nb : reference to the original file is not stored in EZFig so you will not be able to further change its settings, such as contrast or Z Slice, t frame or anything else…).

Import stack from ImageJ : First open a stack or a video in ImageJ (it can be a virtual stack). Then press this button and a copy of the ImagePlus will be stored in your figure. EZFig will still be able to edit image channels, channel colours, select Z slice or t frames.

Save : Saves an “ezf” file, the native file format for EZFig. Please always save your figures in this format as this is the only file format EZFig can reedit and modify.

Save As : Same as “save” but prompts for the output file name.

Exports As : exports the current figure to several file formats (please also see the "Exports" section).

Export to ImageJ : export the current Figure to ImageJ as an ImagePlus.

Export to ImageJ stack : export the current Figure to ImageJ as an ImagePlus containing an ImageStack.

Extract Images from current figure : export images embedded in the current figure to a folder.

7.4) Keep For Later

Keep current selection for later : Use this if you don’t want the selection to appear in the current figure, but nevertheless want to keep it, for example because you plan to use it later. The content of the “Keep For Later” menu is stored in the .ezf file. “kept for later” selected objects appear in this menu as new buttons together with an icon (see Custom content below) and the menu turns red.

Permanently delete all elements stored below (please pay attention, it's irreversible) : Removes all elements from the “Keep For Later” menu (pressing this button erases the content of this menu and therefore these images are no longer saved in the .ezf file), so be careful with this.

Add all elements stored below back to the original figure : Adds back to the figure, the content of the “Keep For Later” menu.

Custom content : The “Keep For Later” menu may contain custom content added by the user. This content is made available as a button, pressing a button adds its content back to the figure.

8.1.2) "Labels" tab

1st letter : put the first letter of the selected figure here and hit "Enter" on your keyboard or press the "Update letters" to get your figure letters incremented automatically. Tip : if you put a space instead of a letter then letters from the selected Figure will be removed.

Add Legend : Adds a text field/legend text row at the end of the selected figure (the text is wrapped automatically) and behaves as a row object.

8.3) "Panel/Montage" objects parameters

8.3.1) "Layout" tab

Number Of Rows : sets the number of rows of the panel (a panel is a 2D table of images).

Number of Columns : sets the number of columns of the panel.

NB : if Number Of Rows * Number of Columns < Number of Images contained in the panel, no change will be made to the panel layout and an error message will be displayed. In that case increasing the numbers of rows or columns or both should get rid of the error message.

Order : defines the order of images in a panel, i.e. should panels be filled horizontally before or after being filled vertically.

8.3.2) "AutoCrops" tab

Since panels are containers that “should” contain only images of the same size (or same aspect ratio) and that might not always be the case, "AutoCrops" contains tools to automatically crop images so that they end up having the same size or the same aspect ratio.

Force Same AR : Force all images contained in the selected panel to have a user defined aspect ratio (to find which AR to use, select a single image with the desired aspect ratio. EZFig will then display the aspect ratio as well as image width and height).

Force Same Width & Height : crops all images in the panel to have them have the same width and height, i.e. have the same size (this achieves a similar result as the Force Same AR function but is likely to crop the images much more, most often you should prefer the Force Same AR function).

Force Same Height : force all images in the panel to have the same height . This does not mean they will have the same AR, so the panel may still look weird.

Force Same Width : force all images in the panel to have the same width. This does not mean they will have the same AR, so the panel may still look weird.

Reset Crops : reset crops for all images in the panel, useful if you made a mistake.

8.4.2) "Crop" tab

Left : defines by which amount the image must be cropped from the left

Right : defines by which amount the image must be cropped from the right

Up : defines by which amount the image must be cropped from the top

Down : defines by which amount the image must be cropped from the bottom

NB: Crops can be used to change image size or aspect ratio, to fit images in panels. Crops can be used to focus on the most interesting region of the image, … Note that the cropped regions are still available in EZFig, they are not discarded, they are just not shown.

Reset Crops : resets crops for selected images.

Same Width : force selected images to have the same width.

Same Height : force selected images to have the same height.

Same Width & Height : force selected images to have same width and height.

8.4.5) "Misc" tab

Make The Selected Image Color Blind Friendly/Split Channels : splits the image to individual gray channels or to pairwise (magenta/green) combinations of channels. This is useful to make the figure colour blind friendly.

Select “Single gray channels and merge” to split image into gray channels and merge. Or press “Magenta green combinations and merge” to get pairwaise (magenta/green) combinations of channels and merge (Select the image and press the “Del” or “Suppr” keyboard keys to remove unwanted combinations). See below for the result of the two types of outputs.

9.2) Change layout

Select the object to be moved, for example a row of the figure (arrow, labelled in cyan). Then press the keyboard "up" or "left" arrow to move the row up. (Press the “Right” or “down” arrows to move a row down).

To move an inner component of the row, click on it until it gets selected (arrow) (see also “Selections” Section). Then press the keyboard "up" or "left" arrow to move an image left (Press the keyboard “down” or “right” arrow to move an image right).

10) Annotating Images

10.1) Add letters, labels and scalebar to an image

Click on an image until you see a red selection around it (left arrow). Most likely you will have to click more than one time (see the “Selections” Section). Upon selection, the image menu appears (middle arrow). Select the "Label" panel then click on the "+Text, scale-bar, ..." button (right arrow).

10.2) Add ROIs/Floating text labels to an image

Click on an image until you see a red selection around it (left arrow), you will most likely have to click more than one time (see the “ Selections” Section). Upon image selection, the image menu appears (middle arrow). Select the "Label" panel then click on the "+ROIs, arrows, text, ..." button (right arrow).

Select the second ROI by clicking on it (left arrow). Then press "ROIs → inset/PIP" (right arrow). A validation message shows upon success. Press "Ok" to close the dialog, then press "Ok" again to close the ROI dialog.

10.4) Add labels outside images/rows

Press “+ text labels above images” (right most arrow). Select “1” for begin and end (middle arrows). This means the label will be over the first image of the row only. Type in your text (bottom arrow).

Labels have been added above images. Labels can also be added left, right and below rows.

11) Keep for later

Often one needs to hide/remove portions of figures that are not yet finalized, however this unfinished work must still be kept somewhere in order to be added back later. This is what the "Keep For Later" menu is for.

Select the object(s) to remove temporarily/hide from the figure. In this example, I selected the bottom right image (lower arrow). Press "Keep For Later > Keep current selection for later" (upper arrow).

Note that the selected image is removed (lower arrow) from the row and added to the "Keep For Later" menu as a button (middle arrow). Note also that the "Keep for later" menu turns red when it contains something (upper arrow).

13.4) Create a panel, add it to a row and change its layout

Duplicate it (i.e. press Ctrl/Cmd + C, Ctrl/Cmd + V) five times (you should have 6 times the same image in your figure). Here I have six identical leaf image but things would work the same with non identical images having the same aspect ratio (e.g. images in a time series, Z slices, ...).

Select one of the copied images, maintain the Ctrl/Cmd keyboard key and click on the three other copied images (Ctrl/Cmd + Click allows for multiple selection). Note the cyan (or red) rectangles indicating the selected images (arrows).

14) Add inset/Picture in picture (PIP) from the local drive

Press the "Add/Replace Inset" button to insert an image from the local hard drive (Left arrow). Note that it is only possible to add one inset per image, note also that many journals ask not to use insets. To remove the inset associated with the image press "Remove Inset" (right arrow).

15.2) Create a new journal style

Enter the journal parameters based on the journal guidelines such as size of a column, size of 2 columns, fonts to use, letter capitalization rules, style rules, text formatting rules, graph rules, … Provide the name of the journal and it’s all set. Please do not hesitate to send me the journal style you generate so that I can add it to EZFig, you'll be credited for this journal and you may really help other people.

16) Editorial Checks

When submitting a manuscript to a journal one needs to obey several editorial guidelines. EZFig can help you.

If the text did not pass the test, a solution will be offered. Feel free to accept it or reject it. Please pay attention to the offered solutions as text checks are irreversible, are programmatically hard to implement and thereby require careful human inspection.

16.6) Check Graphs

Most journals have guideline regarding graphs (for example regarding units, background colours, ...). To check graphs (please note that EZFig can only check graphs generated with FiguR, a tool included in the EZFig package) :

Read the comments regarding your graph, perform changes or ignore suggestions if you think they are not appropriate. If you accept the solution your graphs will be changed (most changes are irreversible).

17) FiguR

Often figures contain graphs and FiguR is a tool to create graphs that can be directly edited by EZFig. FiguR uses R and ggplot2 to draw graphs. The use of ggplot2 is motivated by the fact that this is the only R library (as far as I know) where fonts can be set. Proper font is mandatory for most scientific publications.